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When staging files I usually open a compare editor and verify if I have not added any extra whitespace. If I did do that, I remove it manually by deleting the text using text selection and the backspace key. Once I save, the changes I removed are still visible, but they indicate a zero-line change.
Created attachment 200686 [details] Step 1 : 1 textual change, 2 whitespace-only
Created attachment 200687 [details] Step 2: after manually removing changes
*** This bug has been marked as a duplicate of bug 352576 ***